[{"department":[{"_id":"GaTk"}],"date_created":"2020-02-06T16:09:14Z","date_published":"2021-05-13T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","acknowledgement":"LdA would like to acknowledge the financial support from MIUR-PRIN2017 WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies CAPES and FUNCAP for financial support.","title":"Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches","oa_version":"Preprint","external_id":{"isi":["000704086300015"]},"isi":1,"page":"657-666","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.03.930966"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","year":"2021","status":"public","ec_funded":1,"_id":"7463","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1872-8286"],"issn":["0925-2312"]},"month":"05","author":[{"last_name":"Lombardi","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"last_name":"Shriki","full_name":"Shriki, Oren","first_name":"Oren"},{"last_name":"Herrmann","full_name":"Herrmann, Hans J","first_name":"Hans J"},{"full_name":"de Arcangelis, Lucilla","first_name":"Lucilla","last_name":"de Arcangelis"}],"article_type":"original","fulldoi":"https://doi.org/10.1016/j.neucom.2020.05.126","abstract":[{"lang":"eng","text":"Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms."}],"day":"13","publication_status":"published","type":"journal_article","publication":"Neurocomputing","volume":461,"citation":{"chicago":"Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>.","ista":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. 461, 657–666.","short":"F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.","mla":"Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>, vol. 461, Elsevier, 2021, pp. 657–66, doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>.","ama":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. 2021;461:657-666. doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>","ieee":"F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches,” <i>Neurocomputing</i>, vol. 461. Elsevier, pp. 657–666, 2021.","apa":"Lombardi, F., Shriki, O., Herrmann, H. J., &#38; de Arcangelis, L. (2021). Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>"},"date_updated":"2025-04-14T07:44:02Z","intvolume":"       461","doi":"10.1016/j.neucom.2020.05.126","publisher":"Elsevier","scopus_import":"1","oa":1},{"author":[{"last_name":"Fredes Tolorza","id":"384825DA-F248-11E8-B48F-1D18A9856A87","first_name":"Felipe A","full_name":"Fredes Tolorza, Felipe A"},{"full_name":"Silva Sifuentes, Maria A","first_name":"Maria A","id":"371B3D6E-F248-11E8-B48F-1D18A9856A87","last_name":"Silva Sifuentes"},{"first_name":"Peter","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner"},{"full_name":"Kobayashi, Kenta","first_name":"Kenta","last_name":"Kobayashi"},{"last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi"}],"article_type":"original","file_date_updated":"2020-10-19T13:31:28Z","fulldoi":"https://doi.org/10.1016/j.cub.2020.09.074","abstract":[{"text":"Novelty facilitates formation of memories. The detection of novelty and storage of contextual memories are both mediated by the hippocampus, yet the mechanisms that link these two functions remain to be defined. Dentate granule cells (GCs) of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual memory. However, their key excitatory inputs from the entorhinal cortex are not responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally regulates novelty-induced contextual memory acquisition. Our results show that ventral MCs activity controls memory formation through an intra-hippocampal interaction mechanism gated by novelty.","lang":"eng"}],"day":"11","publication_status":"published","type":"journal_article","volume":31,"publication":"Current Biology","issue":"1","citation":{"chicago":"Fredes Tolorza, Felipe A, Maria A Silva Sifuentes, Peter Koppensteiner, Kenta Kobayashi, Maximilian A Jösch, and Ryuichi Shigemoto. “Ventro-Dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">https://doi.org/10.1016/j.cub.2020.09.074</a>.","mla":"Fredes Tolorza, Felipe A., et al. “Ventro-Dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation.” <i>Current Biology</i>, vol. 31, no. 1, Elsevier, 2021, p. P25–38.E5, doi:<a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">10.1016/j.cub.2020.09.074</a>.","ama":"Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch MA, Shigemoto R. Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. <i>Current Biology</i>. 2021;31(1):P25-38.E5. doi:<a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">10.1016/j.cub.2020.09.074</a>","ista":"Fredes Tolorza FA, Silva Sifuentes MA, Koppensteiner P, Kobayashi K, Jösch MA, Shigemoto R. 2021. Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. Current Biology. 31(1), P25–38.E5.","short":"F.A. Fredes Tolorza, M.A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi, M.A. Jösch, R. Shigemoto, Current Biology 31 (2021) P25–38.E5.","ieee":"F. A. Fredes Tolorza, M. A. Silva Sifuentes, P. Koppensteiner, K. Kobayashi, M. A. Jösch, and R. Shigemoto, “Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation,” <i>Current Biology</i>, vol. 31, no. 1. Elsevier, p. P25–38.E5, 2021.","apa":"Fredes Tolorza, F. A., Silva Sifuentes, M. A., Koppensteiner, P., Kobayashi, K., Jösch, M. A., &#38; Shigemoto, R. (2021). Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2020.09.074\">https://doi.org/10.1016/j.cub.2020.09.074</a>"},"intvolume":"        31","date_updated":"2025-06-12T06:54:22Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1016/j.cub.2020.09.074","scopus_import":"1","publisher":"Elsevier","pmid":1,"oa":1,"department":[{"_id":"MaJö"},{"_id":"RySh"}],"ddc":["570"],"file":[{"checksum":"b7b9c8bc84a08befce365c675229a7d1","success":1,"date_created":"2020-10-19T13:31:28Z","creator":"dernst","file_name":"2021_CurrentBiology_Fredes.pdf","relation":"main_file","file_size":4915964,"access_level":"open_access","file_id":"8678","content_type":"application/pdf","date_updated":"2020-10-19T13:31:28Z"}],"date_created":"2020-02-28T10:56:18Z","date_published":"2021-01-11T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","acknowledgement":"We thank Peter Jonas and Peter Somogyi for critically reading the manuscript, Satoshi Kida for helpful discussion, Taijia Makinen for providing the Prox1-creERT2 mouse line, and Hiromu Yawo for the VAMP2-Venus construct. We also thank Vivek Jayaraman, Ph.D.; Rex A. Kerr, Ph.D.; Douglas S. Kim, Ph.D.; Loren L. Looger, Ph.D.; and Karel Svoboda, Ph.D. from the GENIE Project, Janelia Farm Research Campus, Howard Hughes Medical Institute for the viral constructs used for GCaMP6s expression. We also thank Jacqueline Montanaro, Vanessa Zheden, David Kleindienst, and Laura Burnett for technical assistance, as well as Robert Beattie for imaging assistance. This work was supported by a European Research Council Advanced Grant 694539 to R.S.","title":"Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation","oa_version":"Published Version","related_material":{"link":[{"url":"https://ist.ac.at/en/news/remembering-novelty/","description":"News on IST Homepage","relation":"press_release"}]},"external_id":{"isi":["000614361000020"],"pmid":["33065009"]},"isi":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"P25-38.E5","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694539"}],"quality_controlled":"1","year":"2021","status":"public","ec_funded":1,"_id":"7551","language":[{"iso":"eng"}],"month":"01","has_accepted_license":"1"},{"abstract":[{"lang":"eng","text":"Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart."}],"fulldoi":"https://doi.org/10.1038/s41467-021-25211-4","file_date_updated":"2021-08-10T12:29:59Z","day":"10","publication_status":"published","author":[{"first_name":"Andrea","full_name":"Raso, Andrea","last_name":"Raso"},{"last_name":"Dirkx","first_name":"Ellen","full_name":"Dirkx, Ellen"},{"last_name":"Sampaio-Pinto","first_name":"Vasco","full_name":"Sampaio-Pinto, Vasco"},{"first_name":"Hamid","full_name":"el Azzouzi, Hamid","last_name":"el Azzouzi"},{"full_name":"Cubero, Ryan J","first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","last_name":"Cubero"},{"last_name":"Sorensen","first_name":"Daniel W.","full_name":"Sorensen, Daniel W."},{"last_name":"Ottaviani","full_name":"Ottaviani, Lara","first_name":"Lara"},{"full_name":"Olieslagers, Servé","first_name":"Servé","last_name":"Olieslagers"},{"last_name":"Huibers","first_name":"Manon M.","full_name":"Huibers, Manon M."},{"last_name":"de Weger","full_name":"de Weger, Roel","first_name":"Roel"},{"last_name":"Siddiqi","first_name":"Sailay","full_name":"Siddiqi, Sailay"},{"last_name":"Moimas","full_name":"Moimas, Silvia","first_name":"Silvia"},{"last_name":"Torrini","full_name":"Torrini, Consuelo","first_name":"Consuelo"},{"full_name":"Zentillin, Lorena","first_name":"Lorena","last_name":"Zentillin"},{"full_name":"Braga, Luca","first_name":"Luca","last_name":"Braga"},{"first_name":"Diana S.","full_name":"Nascimento, Diana S.","last_name":"Nascimento"},{"first_name":"Paula A.","full_name":"da Costa Martins, Paula A.","last_name":"da Costa Martins"},{"first_name":"Jop H.","full_name":"van Berlo, Jop H.","last_name":"van Berlo"},{"full_name":"Zacchigna, Serena","first_name":"Serena","last_name":"Zacchigna"},{"first_name":"Mauro","full_name":"Giacca, Mauro","last_name":"Giacca"},{"last_name":"De Windt","first_name":"Leon J.","full_name":"De Windt, Leon J."}],"article_type":"original","doi":"10.1038/s41467-021-25211-4","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2023-08-11T10:27:03Z","intvolume":"        12","oa":1,"pmid":1,"publisher":"Springer Nature","scopus_import":"1","volume":12,"publication":"Nature Communications","type":"journal_article","article_number":"4808","citation":{"ista":"Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 12, 4808.","short":"A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen, L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas, C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H. van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).","mla":"Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>, vol. 12, 4808, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-25211-4\">10.1038/s41467-021-25211-4</a>.","ama":"Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-25211-4\">10.1038/s41467-021-25211-4</a>","chicago":"Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-25211-4\">https://doi.org/10.1038/s41467-021-25211-4</a>.","apa":"Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen, D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-25211-4\">https://doi.org/10.1038/s41467-021-25211-4</a>","ieee":"A. Raso <i>et al.</i>, “A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021."},"article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"external_id":{"isi":["000683910200042"],"pmid":["34376683"]},"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-32785-0","relation":"erratum"}]},"oa_version":"Published Version","title":"A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration","acknowledgement":"E.D. is supported by a VENI award 916-150-16 from the Netherlands Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship (EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number 627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência, Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).","genbank":["GSE178867"],"ddc":["610","570"],"department":[{"_id":"SaSi"}],"date_published":"2021-08-10T00:00:00Z","date_created":"2021-08-10T11:49:20Z","file":[{"relation":"main_file","file_size":4364333,"access_level":"open_access","file_id":"9876","date_updated":"2021-08-10T12:29:59Z","content_type":"application/pdf","checksum":"48d8562e8229e4282f3f354b329722c5","success":1,"date_created":"2021-08-10T12:29:59Z","creator":"asandaue","file_name":"2021_NatureCommunications_Raso.pdf"}],"_id":"9874","has_accepted_license":"1","month":"08","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","status":"public","quality_controlled":"1","year":"2021"},{"date_published":"2021-07-16T00:00:00Z","file":[{"relation":"main_file","file_size":1898360,"access_level":"open_access","date_updated":"2021-08-11T09:31:41Z","content_type":"application/pdf","file_id":"9879","checksum":"19e84ad8c03c60222744ee8e16cd6998","date_created":"2021-08-11T09:31:41Z","success":1,"creator":"asandaue","file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf"}],"date_created":"2021-08-10T19:30:41Z","ddc":["580","570"],"department":[{"_id":"DaZi"}],"external_id":{"pmid":["34272287"],"isi":["000685037700012"]},"isi":1,"title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","acknowledgement":"We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","year":"2021","status":"public","month":"07","has_accepted_license":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"_id":"9877","article_type":"original","author":[{"last_name":"Rodrigues","full_name":"Rodrigues, Jessica A.","first_name":"Jessica A."},{"first_name":"Ping-Hung","full_name":"Hsieh, Ping-Hung","last_name":"Hsieh"},{"first_name":"Deling","full_name":"Ruan, Deling","last_name":"Ruan"},{"first_name":"Toshiro","full_name":"Nishimura, Toshiro","last_name":"Nishimura"},{"last_name":"Sharma","first_name":"Manoj K.","full_name":"Sharma, Manoj K."},{"last_name":"Sharma","first_name":"Rita","full_name":"Sharma, Rita"},{"last_name":"Ye","first_name":"XinYi","full_name":"Ye, XinYi"},{"last_name":"Nguyen","full_name":"Nguyen, Nicholas D.","first_name":"Nicholas D."},{"last_name":"Nijjar","first_name":"Sukhranjan","full_name":"Nijjar, Sukhranjan"},{"first_name":"Pamela C.","full_name":"Ronald, Pamela C.","last_name":"Ronald"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."},{"first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman"}],"publication_status":"published","day":"16","abstract":[{"text":"Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.","lang":"eng"}],"file_date_updated":"2021-08-11T09:31:41Z","fulldoi":"https://doi.org/10.1073/pnas.2104445118","citation":{"ama":"Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(29). doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>","mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>.","ista":"Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences of the United States of America. 118(29), e2104445118.","short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>.","apa":"Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>","ieee":"J. A. Rodrigues <i>et al.</i>, “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 29. National Academy of Sciences, 2021."},"article_number":"e2104445118","issue":"29","type":"journal_article","volume":118,"publication":"Proceedings of the National Academy of Sciences of the United States of America","pmid":1,"oa":1,"scopus_import":"1","publisher":"National Academy of Sciences","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1073/pnas.2104445118","date_updated":"2025-05-14T10:59:43Z","intvolume":"       118"},{"ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"date_published":"2021-08-01T00:00:00Z","date_created":"2021-08-12T07:08:36Z","file":[{"checksum":"d035be2b894c4d50d90ac5ce252e27cd","success":1,"date_created":"2021-10-27T12:57:06Z","creator":"cziletti","file_name":"2021_JMathPhy_Lauritsen.pdf","file_size":4352640,"relation":"main_file","access_level":"open_access","file_id":"10188","content_type":"application/pdf","date_updated":"2021-10-27T12:57:06Z"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2103.07975"],"isi":["000683960800003"]},"isi":1,"acknowledgement":"The author would like to thank Robert Seiringer for guidance and many helpful comments on this project. The author would also like to thank Mathieu Lewin for his comments on the manuscript and Lorenzo Portinale for providing his lecture notes for the course “Mathematics of quantum many-body systems” in spring 2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these lecture notes.","title":"Floating Wigner crystal and periodic jellium configurations","oa_version":"Published Version","year":"2021","quality_controlled":"1","status":"public","_id":"9891","month":"08","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-2488"],"eissn":["1089-7658"]},"author":[{"last_name":"Lauritsen","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"article_type":"original","abstract":[{"text":"Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)], we present a modified “floating crystal” trial state for jellium (also known as the classical homogeneous electron gas) with density equal to a characteristic function. This allows us to show that three definitions of the jellium energy coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache [“Equality of the Jellium and uniform electron gas next-order asymptotic terms for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized energy” studied in a series of papers by Serfaty and others, and thus, by the work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate the jellium energy to the order n term in the logarithmic energy of n points on the unit 2-sphere. We improve upon known lower bounds for this renormalized energy. Additionally, we derive formulas for the jellium energy of periodic configurations.","lang":"eng"}],"corr_author":"1","file_date_updated":"2021-10-27T12:57:06Z","fulldoi":"https://doi.org/10.1063/5.0053494","arxiv":1,"day":"01","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"publication_status":"published","issue":"8","type":"journal_article","publication":"Journal of Mathematical Physics","volume":62,"citation":{"ieee":"A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8. AIP Publishing, 2021.","apa":"Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0053494\">https://doi.org/10.1063/5.0053494</a>","chicago":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0053494\">https://doi.org/10.1063/5.0053494</a>.","ama":"Lauritsen AB. Floating Wigner crystal and periodic jellium configurations. <i>Journal of Mathematical Physics</i>. 2021;62(8). doi:<a href=\"https://doi.org/10.1063/5.0053494\">10.1063/5.0053494</a>","mla":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8, 083305, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0053494\">10.1063/5.0053494</a>.","short":"A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).","ista":"Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 62(8), 083305."},"article_number":"083305","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1063/5.0053494","intvolume":"        62","date_updated":"2024-10-09T21:00:48Z","oa":1,"publisher":"AIP Publishing","scopus_import":"1"},{"volume":127,"publication":"Physical Review Letters","type":"journal_article","issue":"6","article_number":"060602","citation":{"chicago":"Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.060602\">https://doi.org/10.1103/physrevlett.127.060602</a>.","short":"V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).","ista":"Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.","mla":"Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” <i>Physical Review Letters</i>, vol. 127, no. 6, 060602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.060602\">10.1103/physrevlett.127.060602</a>.","ama":"Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces of local Hamiltonians. <i>Physical Review Letters</i>. 2021;127(6). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.060602\">10.1103/physrevlett.127.060602</a>","ieee":"V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from nullspaces of local Hamiltonians,” <i>Physical Review Letters</i>, vol. 127, no. 6. American Physical Society, 2021.","apa":"Karle, V., Serbyn, M., &#38; Michailidis, A. (2021). Area-law entangled eigenstates from nullspaces of local Hamiltonians. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.127.060602\">https://doi.org/10.1103/physrevlett.127.060602</a>"},"date_updated":"2026-04-07T11:48:53Z","intvolume":"       127","doi":"10.1103/physrevlett.127.060602","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publisher":"American Physical Society","scopus_import":"1","oa":1,"author":[{"orcid":"0000-0002-6963-0129","first_name":"Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","full_name":"Karle, Volker","last_name":"Karle"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827"},{"orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","last_name":"Michailidis"}],"article_type":"letter_note","fulldoi":"https://doi.org/10.1103/physrevlett.127.060602","file_date_updated":"2021-08-13T09:28:08Z","abstract":[{"lang":"eng","text":"Eigenstate thermalization in quantum many-body systems implies that eigenstates at high energy are similar to random vectors. Identifying systems where at least some eigenstates are nonthermal is an outstanding question. In this Letter we show that interacting quantum models that have a nullspace—a degenerate subspace of eigenstates at zero energy (zero modes), which corresponds to infinite temperature, provide a route to nonthermal eigenstates. We analytically show the existence of a zero mode which can be represented as a matrix product state for a certain class of local Hamiltonians. In the more general case we use a subspace disentangling algorithm to generate an orthogonal basis of zero modes characterized by increasing entanglement entropy. We show evidence for an area-law entanglement scaling of the least-entangled zero mode in the broad parameter regime, leading to a conjecture that all local Hamiltonians with the nullspace feature zero modes with area-law entanglement scaling and, as such, break the strong thermalization hypothesis. Finally, we find zero modes in constrained models and propose a setup for observing their experimental signatures."}],"publication_status":"published","day":"06","arxiv":1,"status":"public","year":"2021","quality_controlled":"1","project":[{"grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"ec_funded":1,"_id":"9903","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"has_accepted_license":"1","month":"08","department":[{"_id":"MaSe"},{"_id":"GradSch"},{"_id":"MiLe"}],"ddc":["539"],"date_created":"2021-08-13T09:27:39Z","file":[{"file_size":5064231,"relation":"main_file","access_level":"open_access","date_updated":"2021-08-13T09:28:08Z","content_type":"application/pdf","file_id":"9904","checksum":"51218f302dcef99d90d1209809fcc874","date_created":"2021-08-13T09:28:08Z","success":1,"creator":"mserbyn","file_name":"PhysRevLett.127.060602_SOM.pdf"}],"date_published":"2021-08-06T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (in subscription journal)","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19393"}]},"oa_version":"Published Version","title":"Area-law entangled eigenstates from nullspaces of local Hamiltonians","acknowledgement":"We acknowledge useful discussions with V. Gritsev and A. Garkun and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and M. S. were supported by the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)","isi":1,"external_id":{"isi":["000684276000002"],"arxiv":["2102.13633"]}},{"article_number":"8385","citation":{"chicago":"Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling, Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22168385\">https://doi.org/10.3390/ijms22168385</a>.","short":"I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel, A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences 22 (2021).","ista":"Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 22(16), 8385.","mla":"Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 16, 8385, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22168385\">10.3390/ijms22168385</a>.","ama":"Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. <i>International Journal of Molecular Sciences</i>. 2021;22(16). doi:<a href=\"https://doi.org/10.3390/ijms22168385\">10.3390/ijms22168385</a>","ieee":"I. Yotova <i>et al.</i>, “LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 16. MDPI, 2021.","apa":"Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel, L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22168385\">https://doi.org/10.3390/ijms22168385</a>"},"issue":"16","publication":"International Journal of Molecular Sciences","volume":22,"type":"journal_article","oa":1,"pmid":1,"scopus_import":"1","publisher":"MDPI","doi":"10.3390/ijms22168385","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-06-12T06:29:07Z","intvolume":"        22","article_type":"original","author":[{"last_name":"Yotova","full_name":"Yotova, Iveta","first_name":"Iveta"},{"first_name":"Quanah J.","full_name":"Hudson, Quanah J.","last_name":"Hudson"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Proestling","full_name":"Proestling, Katharina","first_name":"Katharina"},{"last_name":"Haslinger","full_name":"Haslinger, Isabella","first_name":"Isabella"},{"first_name":"Lorenz","full_name":"Kuessel, Lorenz","last_name":"Kuessel"},{"last_name":"Perricos","full_name":"Perricos, Alexandra","first_name":"Alexandra"},{"last_name":"Husslein","first_name":"Heinrich","full_name":"Husslein, Heinrich"},{"last_name":"Wenzl","first_name":"René","full_name":"Wenzl, René"}],"day":"04","publication_status":"published","abstract":[{"text":"Endometriosis is a common gynecological disorder characterized by ectopic growth of endometrium outside the uterus and is associated with chronic pain and infertility. We investigated the role of the long intergenic noncoding RNA 01133 (LINC01133) in endometriosis, an lncRNA that has been implicated in several types of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions. As expression appeared higher in the epithelial endometrial layer, we performed a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic assays indicated that LINC01133 may promote proliferation and suppress cellular migration, and affect the cytoskeleton and morphology of the cells. Gene ontology analysis of differentially expressed genes indicated that cell proliferation and migration pathways were affected in line with the observed phenotype. We validated upregulation of p21 and downregulation of Cyclin A at the protein level, which together with the quantification of the DNA content using fluorescence-activated cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation may be due to changes in cell cycle. Further, we found testis-specific protein kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation of actin severing protein Cofilin, which could explain changes in the cytoskeleton and cellular migration. These results indicate that endometriosis is associated with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation and migration pathways.","lang":"eng"}],"fulldoi":"https://doi.org/10.3390/ijms22168385","file_date_updated":"2021-08-16T09:29:17Z","year":"2021","status":"public","quality_controlled":"1","has_accepted_license":"1","month":"08","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"_id":"9906","date_published":"2021-08-04T00:00:00Z","file":[{"file_size":2646018,"relation":"main_file","access_level":"open_access","file_id":"9922","content_type":"application/pdf","date_updated":"2021-08-16T09:29:17Z","checksum":"be7f0042607ca60549cb27513c19c6af","success":1,"date_created":"2021-08-16T09:29:17Z","creator":"asandaue","file_name":"2021_InternationalJournalOfMolecularSciences_Yotova.pdf"}],"date_created":"2021-08-15T22:01:27Z","ddc":["570"],"department":[{"_id":"SiHi"}],"isi":1,"external_id":{"isi":["000689147400001"],"pmid":["34445100"]},"oa_version":"Published Version","title":"LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line","acknowledgement":"Open access funding provided by Medical University of Vienna. The authors would like to thank all the participants and health professionals involved in the present study. We want to thank our technical assistants Barbara Widmar and Matthias Witzmann-Stern for their diligent work and constant assistance. We would like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and resources.","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2025-07-10T12:02:05Z","intvolume":"        22","doi":"10.3390/ijms22158350","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","publisher":"MDPI","oa":1,"pmid":1,"volume":22,"publication":"International Journal of Molecular Sciences","type":"journal_article","issue":"15","article_number":"8350","citation":{"chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>.","mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15, 8350, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>.","ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. 2021;22(15). doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>","short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021).","ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350.","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15. MDPI, 2021.","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., &#38; Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>"},"fulldoi":"https://doi.org/10.3390/ijms22158350","file_date_updated":"2021-08-16T09:35:56Z","abstract":[{"lang":"eng","text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. "}],"day":"01","publication_status":"published","author":[{"first_name":"Naďa","full_name":"Labajová, Naďa","last_name":"Labajová"},{"last_name":"Baranova","full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S.","orcid":"0000-0002-3086-9124"},{"first_name":"Miroslav","full_name":"Jurásek, Miroslav","last_name":"Jurásek"},{"last_name":"Vácha","full_name":"Vácha, Robert","first_name":"Robert"},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barák","first_name":"Imrich","full_name":"Barák, Imrich"}],"article_type":"original","ec_funded":1,"_id":"9907","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"has_accepted_license":"1","month":"08","status":"public","quality_controlled":"1","year":"2021","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"679239","name":"Self-Organization of the Bacterial Cell"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","oa_version":"Published Version","acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","isi":1,"external_id":{"isi":["000681815400001"],"pmid":["34361115"]},"department":[{"_id":"MaLo"}],"ddc":["570"],"file":[{"success":1,"date_created":"2021-08-16T09:35:56Z","checksum":"a4bc06e9a2c803ceff5a91f10b174054","file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","creator":"asandaue","relation":"main_file","file_size":6132410,"file_id":"9923","date_updated":"2021-08-16T09:35:56Z","content_type":"application/pdf","access_level":"open_access"}],"date_created":"2021-08-15T22:01:27Z","date_published":"2021-08-01T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}]},{"date_updated":"2026-04-02T14:05:14Z","intvolume":"        12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.3390/genes12081136","publisher":"MDPI","scopus_import":"1","pmid":1,"oa":1,"type":"journal_article","volume":12,"publication":"Genes","issue":"8","citation":{"ieee":"M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","apa":"Picard, M. A. L., Vicoso, B., Bertrand, S., &#38; Escriva, H. (2021). Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>","chicago":"Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>.","short":"M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).","ista":"Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 12(8), 1136.","mla":"Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>, vol. 12, no. 8, 1136, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>.","ama":"Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>"},"article_number":"1136","file_date_updated":"2021-08-16T09:49:35Z","fulldoi":"https://doi.org/10.3390/genes12081136","abstract":[{"text":"About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems.","lang":"eng"}],"day":"01","publication_status":"published","author":[{"last_name":"Picard","orcid":"0000-0002-8101-2518","first_name":"Marion A L","full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"},{"full_name":"Bertrand, Stéphanie","first_name":"Stéphanie","last_name":"Bertrand"},{"first_name":"Hector","full_name":"Escriva, Hector","last_name":"Escriva"}],"article_type":"review","ec_funded":1,"_id":"9908","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2073-4425"]},"month":"08","has_accepted_license":"1","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257"}],"status":"public","quality_controlled":"1","year":"2021","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"Yes","title":"Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict","oa_version":"Published Version","external_id":{"pmid":["34440310"],"isi":["000690475900001"]},"isi":1,"department":[{"_id":"BeVi"}],"ddc":["570"],"file":[{"file_name":"2021_Genes_Picard.pdf","creator":"asandaue","success":1,"date_created":"2021-08-16T09:49:35Z","checksum":"744e60e56d290a96da3c91a9779f886f","file_id":"9926","content_type":"application/pdf","date_updated":"2021-08-16T09:49:35Z","access_level":"open_access","relation":"main_file","file_size":2297655}],"date_created":"2021-08-15T22:01:27Z","date_published":"2021-08-01T00:00:00Z"},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2073-4425"]},"has_accepted_license":"1","month":"07","_id":"9909","year":"2021","status":"public","quality_controlled":"1","oa_version":"Published Version","title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","isi":1,"external_id":{"isi":["000690558000001"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"Yes","file":[{"access_level":"open_access","date_updated":"2021-08-16T09:02:40Z","content_type":"application/pdf","file_id":"9919","file_size":1340305,"relation":"main_file","creator":"asandaue","file_name":"2021_Genes_Zeng.pdf","checksum":"3d99535618cf9a5b14d264408fa52e97","date_created":"2021-08-16T09:02:40Z","success":1}],"date_created":"2021-08-15T22:01:28Z","date_published":"2021-07-27T00:00:00Z","department":[{"_id":"JiFr"}],"ddc":["580","570"],"publisher":"MDPI","scopus_import":"1","oa":1,"date_updated":"2026-04-02T13:57:06Z","intvolume":"        12","doi":"10.3390/genes12081141","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_number":"1141","citation":{"chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>.","ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>, vol. 12, no. 8, 1141, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>.","short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","ieee":"Y. Zeng <i>et al.</i>, “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>"},"volume":12,"publication":"Genes","type":"journal_article","issue":"8","day":"27","publication_status":"published","fulldoi":"https://doi.org/10.3390/genes12081141","file_date_updated":"2021-08-16T09:02:40Z","abstract":[{"text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.","lang":"eng"}],"article_type":"original","author":[{"last_name":"Zeng","first_name":"Yinwei","full_name":"Zeng, Yinwei"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"first_name":"Hoang Khai","full_name":"Trinh, Hoang Khai","last_name":"Trinh"},{"last_name":"Heugebaert","first_name":"Thomas","full_name":"Heugebaert, Thomas"},{"last_name":"Stevens","first_name":"Christian V.","full_name":"Stevens, Christian V."},{"first_name":"Irene","full_name":"Garcia-Maquilon, Irene","last_name":"Garcia-Maquilon"},{"last_name":"Rodriguez","full_name":"Rodriguez, Pedro L.","first_name":"Pedro L."},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"}]},{"ec_funded":1,"_id":"9910","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1476-5438"],"issn":["1018-4813"]},"has_accepted_license":"1","month":"07","page":"1082-1091","year":"2021","quality_controlled":"1","status":"public","project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","acknowledgement":"We are grateful to Marianna Bevova and Pavel Borodin for fruitful discussion and help with conceptualising our findings and to Lennart C. Karssen for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects in control of complex human traits”). The work of SAS, IAK, and TIS were supported by Russian Ministry of Science and Education under the 5–100 Excellence Programme. The work of YSA and TIA was supported by the Ministry of Education and Science of the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4). FAK is supported by the ERC Consolidator Grant (ChrFL: 771209).","title":"The limits of normal approximation for adult height","isi":1,"external_id":{"pmid":["33664501"],"isi":["000625853200001"]},"department":[{"_id":"FyKo"}],"ddc":["576"],"date_created":"2021-08-15T22:01:28Z","file":[{"access_level":"open_access","file_id":"9921","date_updated":"2021-08-16T09:14:36Z","content_type":"application/pdf","relation":"main_file","file_size":1079395,"creator":"asandaue","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","checksum":"a676d76f91b0dbe0504c63e469129c2a","success":1,"date_created":"2021-08-16T09:14:36Z"}],"date_published":"2021-07-01T00:00:00Z","intvolume":"        29","date_updated":"2025-07-10T12:02:05Z","doi":"10.1038/s41431-021-00836-7","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publisher":"Springer Nature","scopus_import":"1","oa":1,"pmid":1,"publication":"European Journal of Human Genetics","volume":29,"type":"journal_article","issue":"7","citation":{"ieee":"S. A. Slavskii <i>et al.</i>, “The limits of normal approximation for adult height,” <i>European Journal of Human Genetics</i>, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021.","apa":"Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., &#38; Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>","chicago":"Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>.","short":"S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.","ista":"Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091.","mla":"Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>.","ama":"Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. 2021;29(7):1082-1091. doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>"},"fulldoi":"https://doi.org/10.1038/s41431-021-00836-7","file_date_updated":"2021-08-16T09:14:36Z","abstract":[{"lang":"eng","text":"Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait."}],"day":"01","publication_status":"published","author":[{"last_name":"Slavskii","first_name":"Sergei A.","full_name":"Slavskii, Sergei A."},{"last_name":"Kuznetsov","first_name":"Ivan A.","full_name":"Kuznetsov, Ivan A."},{"last_name":"Shashkova","first_name":"Tatiana I.","full_name":"Shashkova, Tatiana I."},{"full_name":"Bazykin, Georgii A.","first_name":"Georgii A.","last_name":"Bazykin"},{"last_name":"Axenovich","first_name":"Tatiana I.","full_name":"Axenovich, Tatiana I."},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"last_name":"Aulchenko","first_name":"Yurii S.","full_name":"Aulchenko, Yurii S."}],"article_type":"original"},{"year":"2021","quality_controlled":"1","status":"public","page":"56-73","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jmi.13041"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"month":"08","_id":"9911","date_created":"2021-08-15T22:01:29Z","date_published":"2021-08-11T00:00:00Z","department":[{"_id":"Bio"}],"ddc":["600"],"oa_version":"Published Version","acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","isi":1,"external_id":{"isi":["000683702700001"],"pmid":["34214188"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","citation":{"short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.","ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. 2021;284(1):56-73. doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>","mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>.","chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>.","apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. Wiley. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>","ieee":"G. Nelson <i>et al.</i>, “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” <i>Journal of Microscopy</i>, vol. 284, no. 1. Wiley, pp. 56–73, 2021."},"volume":284,"publication":"Journal of Microscopy","type":"journal_article","issue":"1","scopus_import":"1","publisher":"Wiley","oa":1,"pmid":1,"date_updated":"2026-06-18T19:59:18Z","intvolume":"       284","doi":"10.1111/jmi.13041","article_type":"original","author":[{"last_name":"Nelson","first_name":"Glyn","full_name":"Nelson, Glyn"},{"last_name":"Boehm","full_name":"Boehm, Ulrike","first_name":"Ulrike"},{"full_name":"Bagley, Steve","first_name":"Steve","last_name":"Bagley"},{"last_name":"Bajcsy","first_name":"Peter","full_name":"Bajcsy, Peter"},{"last_name":"Bischof","full_name":"Bischof, Johanna","first_name":"Johanna"},{"last_name":"Brown","full_name":"Brown, Claire M.","first_name":"Claire M."},{"first_name":"Aurélien","full_name":"Dauphin, Aurélien","last_name":"Dauphin"},{"last_name":"Dobbie","full_name":"Dobbie, Ian M.","first_name":"Ian M."},{"last_name":"Eriksson","first_name":"John E.","full_name":"Eriksson, John E."},{"full_name":"Faklaris, Orestis","first_name":"Orestis","last_name":"Faklaris"},{"first_name":"Julia","full_name":"Fernandez-Rodriguez, Julia","last_name":"Fernandez-Rodriguez"},{"last_name":"Ferrand","first_name":"Alexia","full_name":"Ferrand, Alexia"},{"last_name":"Gelman","first_name":"Laurent","full_name":"Gelman, Laurent"},{"full_name":"Gheisari, Ali","first_name":"Ali","last_name":"Gheisari"},{"first_name":"Hella","full_name":"Hartmann, Hella","last_name":"Hartmann"},{"last_name":"Kukat","full_name":"Kukat, Christian","first_name":"Christian"},{"last_name":"Laude","first_name":"Alex","full_name":"Laude, Alex"},{"full_name":"Mitkovski, Miso","first_name":"Miso","last_name":"Mitkovski"},{"first_name":"Sebastian","full_name":"Munck, Sebastian","last_name":"Munck"},{"last_name":"North","first_name":"Alison J.","full_name":"North, Alison J."},{"first_name":"Tobias M.","full_name":"Rasse, Tobias M.","last_name":"Rasse"},{"first_name":"Ute","full_name":"Resch-Genger, Ute","last_name":"Resch-Genger"},{"full_name":"Schuetz, Lucas C.","first_name":"Lucas C.","last_name":"Schuetz"},{"full_name":"Seitz, Arne","first_name":"Arne","last_name":"Seitz"},{"last_name":"Strambio-De-Castillia","full_name":"Strambio-De-Castillia, Caterina","first_name":"Caterina"},{"last_name":"Swedlow","first_name":"Jason R.","full_name":"Swedlow, Jason R."},{"last_name":"Alexopoulos","first_name":"Ioannis","full_name":"Alexopoulos, Ioannis"},{"first_name":"Karin","full_name":"Aumayr, Karin","last_name":"Aumayr"},{"last_name":"Avilov","first_name":"Sergiy","full_name":"Avilov, Sergiy"},{"last_name":"Bakker","first_name":"Gert Jan","full_name":"Bakker, Gert Jan"},{"last_name":"Bammann","full_name":"Bammann, Rodrigo R.","first_name":"Rodrigo R."},{"full_name":"Bassi, Andrea","first_name":"Andrea","last_name":"Bassi"},{"full_name":"Beckert, Hannes","first_name":"Hannes","last_name":"Beckert"},{"full_name":"Beer, Sebastian","first_name":"Sebastian","last_name":"Beer"},{"first_name":"Yury","full_name":"Belyaev, Yury","last_name":"Belyaev"},{"last_name":"Bierwagen","full_name":"Bierwagen, Jakob","first_name":"Jakob"},{"first_name":"Konstantin A.","full_name":"Birngruber, Konstantin A.","last_name":"Birngruber"},{"last_name":"Bosch","first_name":"Manel","full_name":"Bosch, Manel"},{"first_name":"Juergen","full_name":"Breitlow, Juergen","last_name":"Breitlow"},{"first_name":"Lisa A.","full_name":"Cameron, Lisa A.","last_name":"Cameron"},{"last_name":"Chalfoun","full_name":"Chalfoun, Joe","first_name":"Joe"},{"first_name":"James J.","full_name":"Chambers, James J.","last_name":"Chambers"},{"first_name":"Chieh Li","full_name":"Chen, Chieh Li","last_name":"Chen"},{"last_name":"Conde-Sousa","full_name":"Conde-Sousa, Eduardo","first_name":"Eduardo"},{"last_name":"Corbett","full_name":"Corbett, Alexander D.","first_name":"Alexander D."},{"last_name":"Cordelieres","full_name":"Cordelieres, Fabrice P.","first_name":"Fabrice P."},{"full_name":"Nery, Elaine Del","first_name":"Elaine Del","last_name":"Nery"},{"full_name":"Dietzel, Ralf","first_name":"Ralf","last_name":"Dietzel"},{"full_name":"Eismann, Frank","first_name":"Frank","last_name":"Eismann"},{"full_name":"Fazeli, Elnaz","first_name":"Elnaz","last_name":"Fazeli"},{"first_name":"Andreas","full_name":"Felscher, Andreas","last_name":"Felscher"},{"last_name":"Fried","full_name":"Fried, Hans","first_name":"Hans"},{"first_name":"Nathalie","full_name":"Gaudreault, Nathalie","last_name":"Gaudreault"},{"last_name":"Goh","first_name":"Wah Ing","full_name":"Goh, Wah Ing"},{"last_name":"Guilbert","full_name":"Guilbert, Thomas","first_name":"Thomas"},{"last_name":"Hadleigh","full_name":"Hadleigh, Roland","first_name":"Roland"},{"last_name":"Hemmerich","full_name":"Hemmerich, Peter","first_name":"Peter"},{"first_name":"Gerhard A.","full_name":"Holst, Gerhard A.","last_name":"Holst"},{"full_name":"Itano, Michelle S.","first_name":"Michelle S.","last_name":"Itano"},{"full_name":"Jaffe, Claudia B.","first_name":"Claudia B.","last_name":"Jaffe"},{"first_name":"Helena K.","full_name":"Jambor, Helena K.","last_name":"Jambor"},{"last_name":"Jarvis","full_name":"Jarvis, Stuart C.","first_name":"Stuart C."},{"full_name":"Keppler, Antje","first_name":"Antje","last_name":"Keppler"},{"first_name":"David","full_name":"Kirchenbuechler, David","last_name":"Kirchenbuechler"},{"first_name":"Marcel","full_name":"Kirchner, Marcel","last_name":"Kirchner"},{"last_name":"Kobayashi","first_name":"Norio","full_name":"Kobayashi, Norio"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"last_name":"Kunis","first_name":"Susanne","full_name":"Kunis, Susanne"},{"last_name":"Lacoste","full_name":"Lacoste, Judith","first_name":"Judith"},{"full_name":"Marcello, Marco","first_name":"Marco","last_name":"Marcello"},{"full_name":"Martins, Gabriel G.","first_name":"Gabriel G.","last_name":"Martins"},{"last_name":"Metcalf","full_name":"Metcalf, Daniel J.","first_name":"Daniel J."},{"first_name":"Claire A.","full_name":"Mitchell, Claire A.","last_name":"Mitchell"},{"last_name":"Moore","first_name":"Joshua","full_name":"Moore, Joshua"},{"full_name":"Mueller, Tobias","first_name":"Tobias","last_name":"Mueller"},{"full_name":"Nelson, Michael S.","first_name":"Michael S.","last_name":"Nelson"},{"last_name":"Ogg","full_name":"Ogg, Stephen","first_name":"Stephen"},{"last_name":"Onami","full_name":"Onami, Shuichi","first_name":"Shuichi"},{"last_name":"Palmer","full_name":"Palmer, Alexandra L.","first_name":"Alexandra L."},{"last_name":"Paul-Gilloteaux","full_name":"Paul-Gilloteaux, Perrine","first_name":"Perrine"},{"full_name":"Pimentel, Jaime A.","first_name":"Jaime A.","last_name":"Pimentel"},{"last_name":"Plantard","full_name":"Plantard, Laure","first_name":"Laure"},{"first_name":"Santosh","full_name":"Podder, Santosh","last_name":"Podder"},{"last_name":"Rexhepaj","first_name":"Elton","full_name":"Rexhepaj, Elton"},{"last_name":"Royon","full_name":"Royon, Arnaud","first_name":"Arnaud"},{"last_name":"Saari","full_name":"Saari, Markku A.","first_name":"Markku A."},{"last_name":"Schapman","full_name":"Schapman, Damien","first_name":"Damien"},{"first_name":"Vincent","full_name":"Schoonderwoert, Vincent","last_name":"Schoonderwoert"},{"first_name":"Britta","full_name":"Schroth-Diez, Britta","last_name":"Schroth-Diez"},{"full_name":"Schwartz, Stanley","first_name":"Stanley","last_name":"Schwartz"},{"last_name":"Shaw","full_name":"Shaw, Michael","first_name":"Michael"},{"last_name":"Spitaler","first_name":"Martin","full_name":"Spitaler, Martin"},{"last_name":"Stoeckl","full_name":"Stoeckl, Martin T.","first_name":"Martin T."},{"full_name":"Sudar, Damir","first_name":"Damir","last_name":"Sudar"},{"last_name":"Teillon","first_name":"Jeremie","full_name":"Teillon, Jeremie"},{"last_name":"Terjung","first_name":"Stefan","full_name":"Terjung, Stefan"},{"full_name":"Thuenauer, Roland","first_name":"Roland","last_name":"Thuenauer"},{"last_name":"Wilms","full_name":"Wilms, Christian D.","first_name":"Christian D."},{"last_name":"Wright","first_name":"Graham D.","full_name":"Wright, Graham D."},{"last_name":"Nitschke","full_name":"Nitschke, Roland","first_name":"Roland"}],"day":"11","publication_status":"published","fulldoi":"https://doi.org/10.1111/jmi.13041","abstract":[{"text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.","lang":"eng"}]},{"publisher":"Springer Nature","scopus_import":"1","oa":1,"date_updated":"2025-04-15T08:04:59Z","intvolume":"        22","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1007/s00023-021-01085-6","citation":{"mla":"Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational Functions.” <i>Annales Henri Poincaré </i>, vol. 22, Springer Nature, 2021, pp. 4205–4269, doi:<a href=\"https://doi.org/10.1007/s00023-021-01085-6\">10.1007/s00023-021-01085-6</a>.","ama":"Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative rational functions. <i>Annales Henri Poincaré </i>. 2021;22:4205–4269. doi:<a href=\"https://doi.org/10.1007/s00023-021-01085-6\">10.1007/s00023-021-01085-6</a>","ista":"Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 22, 4205–4269.","short":"L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré  22 (2021) 4205–4269.","chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum Dots via Noncommutative Rational Functions.” <i>Annales Henri Poincaré </i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00023-021-01085-6\">https://doi.org/10.1007/s00023-021-01085-6</a>.","apa":"Erdös, L., Krüger, T. H., &#38; Nemish, Y. (2021). Scattering in quantum dots via noncommutative rational functions. <i>Annales Henri Poincaré </i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-021-01085-6\">https://doi.org/10.1007/s00023-021-01085-6</a>","ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative rational functions,” <i>Annales Henri Poincaré </i>, vol. 22. Springer Nature, pp. 4205–4269, 2021."},"type":"journal_article","publication":"Annales Henri Poincaré ","volume":22,"publication_status":"published","arxiv":1,"day":"01","file_date_updated":"2022-05-12T12:50:27Z","fulldoi":"https://doi.org/10.1007/s00023-021-01085-6","abstract":[{"lang":"eng","text":"In the customary random matrix model for transport in quantum dots with M internal degrees of freedom coupled to a chaotic environment via 𝑁≪𝑀 channels, the density 𝜌 of transmission eigenvalues is computed from a specific invariant ensemble for which explicit formula for the joint probability density of all eigenvalues is available. We revisit this problem in the large N regime allowing for (i) arbitrary ratio 𝜙:=𝑁/𝑀≤1; and (ii) general distributions for the matrix elements of the Hamiltonian of the quantum dot. In the limit 𝜙→0, we recover the formula for the density 𝜌 that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special matrix ensemble. We also prove that the inverse square root singularity of the density at zero and full transmission in Beenakker’s formula persists for any 𝜙<1 but in the borderline case 𝜙=1 an anomalous 𝜆−2/3 singularity arises at zero. To access this level of generality, we develop the theory of global and local laws on the spectral density of a large class of noncommutative rational expressions in large random matrices with i.i.d. entries."}],"article_type":"original","author":[{"orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","last_name":"Erdös"},{"last_name":"Krüger","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"},{"first_name":"Yuriy","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","full_name":"Nemish, Yuriy","orcid":"0000-0002-7327-856X","last_name":"Nemish"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1424-0661"],"issn":["1424-0637"]},"month":"12","has_accepted_license":"1","ec_funded":1,"_id":"9912","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","year":"2021","status":"public","page":"4205–4269","acknowledgement":"The authors are very grateful to Yan Fyodorov for discussions on the physical background and for providing references, and to the anonymous referee for numerous valuable remarks.","title":"Scattering in quantum dots via noncommutative rational functions","oa_version":"Published Version","external_id":{"arxiv":["1911.05112"],"isi":["000681531500001"]},"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (in subscription journal)","date_created":"2021-08-15T22:01:29Z","file":[{"checksum":"8d6bac0e2b0a28539608b0538a8e3b38","date_created":"2022-05-12T12:50:27Z","success":1,"creator":"dernst","file_name":"2021_AnnHenriPoincare_Erdoes.pdf","relation":"main_file","file_size":1162454,"access_level":"open_access","date_updated":"2022-05-12T12:50:27Z","content_type":"application/pdf","file_id":"11365"}],"date_published":"2021-12-01T00:00:00Z","department":[{"_id":"LaEr"}],"ddc":["510"]},{"publisher":"Institute of Science and Technology Austria","oa":1,"degree_awarded":"PhD","date_updated":"2026-04-15T06:43:02Z","doi":"10.15479/at:ista:9920","alternative_title":["ISTA Thesis"],"citation":{"ieee":"M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021.","apa":"Peruzzo, M. (2021). <i>Geometric superinductors and their applications in circuit quantum electrodynamics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9920\">https://doi.org/10.15479/at:ista:9920</a>","chicago":"Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9920\">https://doi.org/10.15479/at:ista:9920</a>.","ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9920\">10.15479/at:ista:9920</a>","mla":"Peruzzo, Matilda. <i>Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9920\">10.15479/at:ista:9920</a>.","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria."},"type":"dissertation","keyword":["quantum computing","superinductor","quantum metrology"],"publication_status":"published","day":"19","fulldoi":"https://doi.org/10.15479/at:ista:9920","supervisor":[{"last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-09-06T08:39:47Z","OA_place":"publisher","corr_author":"1","abstract":[{"lang":"eng","text":"This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented."}],"author":[{"orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda","first_name":"Matilda","last_name":"Peruzzo"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-013-8"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"08","_id":"9920","year":"2021","status":"public","page":"149","related_material":{"record":[{"id":"9928","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8755"}]},"oa_version":"Published Version","title":"Geometric superinductors and their applications in circuit quantum electrodynamics","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","file":[{"creator":"mperuzzo","file_name":"GeometricSuperinductorsForCQED.zip","checksum":"3cd1986efde5121d7581f6fcf9090da8","date_created":"2021-08-16T09:33:21Z","access_level":"closed","file_id":"9924","date_updated":"2021-09-06T08:39:47Z","content_type":"application/x-zip-compressed","file_size":151387283,"relation":"source_file"},{"file_size":17596344,"relation":"main_file","access_level":"open_access","file_id":"9939","content_type":"application/pdf","date_updated":"2021-09-06T08:39:47Z","checksum":"50928c621cdf0775d7a5906b9dc8602c","date_created":"2021-08-18T14:20:06Z","creator":"mperuzzo","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf"},{"creator":"mperuzzo","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","checksum":"37f486aa1b622fe44af00d627ec13f6c","date_created":"2021-08-18T14:20:09Z","access_level":"closed","content_type":"application/pdf","date_updated":"2021-09-06T08:39:47Z","file_id":"9940","relation":"other","file_size":17592425,"description":"Extra copy of the thesis as PDF/A-2b"}],"date_created":"2021-08-16T09:44:09Z","date_published":"2021-08-19T00:00:00Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"ddc":["539"]},{"publisher":"Association for Computing Machinery","scopus_import":"1","oa":1,"date_updated":"2025-04-14T07:43:49Z","doi":"10.1145/3465084.3467903","citation":{"chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Component Stability in Low-Space Massively Parallel Computation.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 481–491. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467903\">https://doi.org/10.1145/3465084.3467903</a>.","mla":"Czumaj, Artur, et al. “Component Stability in Low-Space Massively Parallel Computation.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 481–491, doi:<a href=\"https://doi.org/10.1145/3465084.3467903\">10.1145/3465084.3467903</a>.","ama":"Czumaj A, Davies P, Parter M. Component stability in low-space massively parallel computation. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:481–491. doi:<a href=\"https://doi.org/10.1145/3465084.3467903\">10.1145/3465084.3467903</a>","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 481–491.","ista":"Czumaj A, Davies P, Parter M. 2021. Component stability in low-space massively parallel computation. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 481–491.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Component stability in low-space massively parallel computation,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 481–491.","apa":"Czumaj, A., Davies, P., &#38; Parter, M. (2021). Component stability in low-space massively parallel computation. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 481–491). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467903\">https://doi.org/10.1145/3465084.3467903</a>"},"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","type":"conference","arxiv":1,"day":"21","publication_status":"published","conference":{"name":"PODC: Principles of Distributed Computing","location":"Virtual, Italy","start_date":"2021-07-26","end_date":"2021-07-30"},"fulldoi":"https://doi.org/10.1145/3465084.3467903","abstract":[{"text":"In this paper, we study the power and limitations of component-stable algorithms in the low-space model of Massively Parallel Computation (MPC). Recently Ghaffari, Kuhn and Uitto (FOCS 2019) introduced the class of component-stable low-space MPC algorithms, which are, informally, defined as algorithms for which the outputs reported by the nodes in different connected components are required to be independent. This very natural notion was introduced to capture most (if not all) of the known efficient MPC algorithms to date, and it was the first general class of MPC algorithms for which one can show non-trivial conditional lower bounds. In this paper we enhance the framework of component-stable algorithms and investigate its effect on the complexity of randomized and deterministic low-space MPC. Our key contributions include: 1) We revise and formalize the lifting approach of Ghaffari, Kuhn and Uitto. This requires a very delicate amendment of the notion of component stability, which allows us to fill in gaps in the earlier arguments. 2) We also extend the framework to obtain conditional lower bounds for deterministic algorithms and fine-grained lower bounds that depend on the maximum degree Δ. 3) We demonstrate a collection of natural graph problems for which non-component-stable algorithms break the conditional lower bound obtained for component-stable algorithms. This implies that, for both deterministic and randomized algorithms, component-stable algorithms are conditionally weaker than the non-component-stable ones.\r\n\r\nAltogether our results imply that component-stability might limit the computational power of the low-space MPC model, paving the way for improved upper bounds that escape the conditional lower bound setting of Ghaffari, Kuhn, and Uitto.","lang":"eng"}],"author":[{"last_name":"Czumaj","full_name":"Czumaj, Artur","first_name":"Artur"},{"orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","full_name":"Davies, Peter","first_name":"Peter","last_name":"Davies"},{"full_name":"Parter, Merav","first_name":"Merav","last_name":"Parter"}],"publication_identifier":{"isbn":["9781450385480"]},"language":[{"iso":"eng"}],"month":"07","ec_funded":1,"_id":"9933","quality_controlled":"1","year":"2021","status":"public","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"page":"481–491","main_file_link":[{"url":"https://arxiv.org/abs/2106.01880","open_access":"1"}],"oa_version":"Submitted Version","title":"Component stability in low-space massively parallel computation","acknowledgement":"This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411.","isi":1,"external_id":{"arxiv":["2106.01880"],"isi":["000744439800049"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","date_created":"2021-08-17T18:11:16Z","date_published":"2021-07-21T00:00:00Z","department":[{"_id":"DaAl"}]},{"year":"2021","quality_controlled":"1","status":"public","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"main_file_link":[{"open_access":"1","url":"http://wrap.warwick.ac.uk/153753"}],"page":"469–479","month":"07","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-8548-0"]},"_id":"9935","ec_funded":1,"date_published":"2021-07-21T00:00:00Z","date_created":"2021-08-17T18:14:15Z","department":[{"_id":"DaAl"}],"isi":1,"external_id":{"isi":["000744439800048"]},"oa_version":"Submitted Version","acknowledgement":"This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411.","title":"Improved deterministic (Δ+1) coloring in low-space MPC","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Czumaj A, Davies P, Parter M. Improved deterministic (Δ+1) coloring in low-space MPC. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:469–479. doi:<a href=\"https://doi.org/10.1145/3465084.3467937\">10.1145/3465084.3467937</a>","mla":"Czumaj, Artur, et al. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 469–479, doi:<a href=\"https://doi.org/10.1145/3465084.3467937\">10.1145/3465084.3467937</a>.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 469–479.","ista":"Czumaj A, Davies P, Parter M. 2021. Improved deterministic (Δ+1) coloring in low-space MPC. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 469–479.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 469–479. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467937\">https://doi.org/10.1145/3465084.3467937</a>.","apa":"Czumaj, A., Davies, P., &#38; Parter, M. (2021). Improved deterministic (Δ+1) coloring in low-space MPC. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 469–479). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467937\">https://doi.org/10.1145/3465084.3467937</a>","ieee":"A. Czumaj, P. Davies, and M. Parter, “Improved deterministic (Δ+1) coloring in low-space MPC,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 469–479."},"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","type":"conference","oa":1,"publisher":"Association for Computing Machinery","scopus_import":"1","doi":"10.1145/3465084.3467937","date_updated":"2025-04-14T07:43:49Z","author":[{"full_name":"Czumaj, Artur","first_name":"Artur","last_name":"Czumaj"},{"last_name":"Davies","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","full_name":"Davies, Peter","first_name":"Peter"},{"full_name":"Parter, Merav","first_name":"Merav","last_name":"Parter"}],"publication_status":"published","conference":{"end_date":"2021-07-30","start_date":"2021-07-26","location":"Virtual, Italy","name":"PODC: Symposium on Principles of Distributed Computing"},"day":"21","abstract":[{"lang":"eng","text":"We present a deterministic O(log log log n)-round low-space Massively Parallel Computation (MPC) algorithm for the classical problem of (Δ+1)-coloring on n-vertex graphs. In this model, every machine has sublinear local space of size n^φ for any arbitrary constant φ \\in (0,1). Our algorithm works under the relaxed setting where each machine is allowed to perform exponential local computations, while respecting the n^φ space and bandwidth limitations.\r\n\r\nOur key technical contribution is a novel derandomization of the ingenious (Δ+1)-coloring local algorithm by Chang-Li-Pettie (STOC 2018, SIAM J. Comput. 2020). The Chang-Li-Pettie algorithm runs in T_local =poly(loglog n) rounds, which sets the state-of-the-art randomized round complexity for the problem in the local model. Our derandomization employs a combination of tools, notably pseudorandom generators (PRG) and bounded-independence hash functions.\r\n\r\nThe achieved round complexity of O(logloglog n) rounds matches the bound of log(T_local ), which currently serves an upper bound barrier for all known randomized algorithms for locally-checkable problems in this model. Furthermore, no deterministic sublogarithmic low-space MPC algorithms for the (Δ+1)-coloring problem have been known before."}],"fulldoi":"https://doi.org/10.1145/3465084.3467937"},{"has_accepted_license":"1","month":"09","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"_id":"9946","year":"2021","status":"public","project":[{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"17","oa_version":"Published Version","related_material":{"record":[{"relation":"shorter_version","status":"public","id":"10108"},{"id":"9281","status":"public","relation":"other"}]},"acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","title":"Differential monitoring","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2021-09-01T00:00:00Z","date_created":"2021-08-20T20:00:37Z","file":[{"file_size":"320453","relation":"main_file","access_level":"open_access","date_updated":"2021-09-03T12:34:28Z","content_type":"application/pdf","file_id":"9948","checksum":"0f9aafd59444cb6bdca6925d163ab946","date_created":"2021-08-20T19:59:44Z","creator":"fmuehlbo","file_name":"differentialmonitoring-techreport.pdf"}],"ddc":["005"],"department":[{"_id":"ToHe"}],"oa":1,"publisher":"IST Austria","doi":"10.15479/AT:ISTA:9946","date_updated":"2025-04-15T06:55:00Z","alternative_title":["IST Austria Technical Report"],"citation":{"ama":"Mühlböck F, Henzinger TA. <i>Differential Monitoring</i>. IST Austria; 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9946\">10.15479/AT:ISTA:9946</a>","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. <i>Differential Monitoring</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9946\">10.15479/AT:ISTA:9946</a>.","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p.","short":"F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. <i>Differential Monitoring</i>. IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9946\">https://doi.org/10.15479/AT:ISTA:9946</a>.","apa":"Mühlböck, F., &#38; Henzinger, T. A. (2021). <i>Differential monitoring</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9946\">https://doi.org/10.15479/AT:ISTA:9946</a>","ieee":"F. Mühlböck and T. A. Henzinger, <i>Differential monitoring</i>. IST Austria, 2021."},"type":"technical_report","keyword":["run-time verification","software engineering","implicit specification"],"day":"01","publication_status":"published","abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:9946","file_date_updated":"2021-09-03T12:34:28Z","author":[{"last_name":"Mühlböck","orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian","first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}]},{"doi":"10.15479/AT:ISTA:9949","_id":"9949","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-04-15T07:49:47Z","has_accepted_license":"1","oa":1,"month":"08","publisher":"Institute of Science and Technology Austria","type":"research_data","status":"public","year":"2021","citation":{"ama":"Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>","mla":"Vicoso, Beatriz. <i>Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>.","short":"B. Vicoso, (2021).","ista":"Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>.","chicago":"Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">https://doi.org/10.15479/AT:ISTA:9949</a>.","apa":"Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">https://doi.org/10.15479/AT:ISTA:9949</a>","ieee":"B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021."},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.15479/AT:ISTA:9949","file_date_updated":"2021-08-21T13:43:59Z","day":"24","oa_version":"None","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10166"}]},"title":"Data from Hyulmans et al 2021, \"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp\"","author":[{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"department":[{"_id":"BeVi"}],"date_published":"2021-08-24T00:00:00Z","date_created":"2021-08-21T13:44:22Z","file":[{"creator":"bvicoso","file_name":"Data.zip","checksum":"90461837eed66beac6fa302993cf0ca9","success":1,"date_created":"2021-08-21T13:43:59Z","access_level":"open_access","file_id":"9950","date_updated":"2021-08-21T13:43:59Z","content_type":"application/zip","file_size":139188306,"relation":"main_file"}]},{"author":[{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"last_name":"Töpfer","first_name":"Martin","full_name":"Töpfer, Martin","id":"4B865388-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Przemysław","full_name":"Uznański, Przemysław","last_name":"Uznański"}],"fulldoi":"https://doi.org/10.1145/3465084.3467915","abstract":[{"text":"There has recently been a surge of interest in the computational and complexity properties of the population model, which assumes n anonymous, computationally-bounded nodes, interacting at random, with the goal of jointly computing global predicates. Significant work has gone towards investigating majority or consensus dynamics in this model: that is, assuming that every node is initially in one of two states X or Y, determine which state had higher initial count.\r\n\r\nIn this paper, we consider a natural generalization of majority/consensus, which we call comparison : in its simplest formulation, we are given two baseline states, X and Y, present in any initial configuration in fixed, but possibly small counts. One of these states has higher count than the other: we will assume |X_0| > C |Y_0| for some constant C > 1. The challenge is to design a protocol by which nodes can quickly and reliably decide on which of the baseline states X_0 and Y_0 has higher initial count. We begin by analyzing a simple and general dynamics solving the above comparison problem, which uses O( log n ) states per node, and converges in O(log n) (parallel) time, with high probability, to a state where the whole population votes on opinions X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|. We then describe how this procedure can be bootstrapped to solve comparison, i.e. have every node in the population reach the \"correct'' decision, with probability 1 - o(1), at the cost of O (log log n) additional states. Further, we prove that this dynamics is self-stabilizing, in the sense that it converges to the correct decision from arbitrary initial states, and leak-robust, in the sense that it can withstand spurious faulty reactions, which are known to occur in practical implementations of population protocols. Our analysis is based on a new martingale concentration result relating the discrete-time evolution of a population protocol to its expected (steady-state) analysis, which should be a useful tool when analyzing opinion dynamics and epidemic dissemination in the population model.","lang":"eng"}],"day":"21","publication_status":"published","conference":{"end_date":"2021-07-30","start_date":"2021-07-26","location":"Virtual, Italy","name":"PODC: Symposium on Principles of Distributed Computing"},"type":"conference","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","citation":{"ista":"Alistarh D-A, Töpfer M, Uznański P. 2021. Comparison dynamics in population protocols. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 55–65.","short":"D.-A. Alistarh, M. Töpfer, P. Uznański, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 55–65.","ama":"Alistarh D-A, Töpfer M, Uznański P. Comparison dynamics in population protocols. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:55-65. doi:<a href=\"https://doi.org/10.1145/3465084.3467915\">10.1145/3465084.3467915</a>","mla":"Alistarh, Dan-Adrian, et al. “Comparison Dynamics in Population Protocols.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 55–65, doi:<a href=\"https://doi.org/10.1145/3465084.3467915\">10.1145/3465084.3467915</a>.","chicago":"Alistarh, Dan-Adrian, Martin Töpfer, and Przemysław Uznański. “Comparison Dynamics in Population Protocols.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 55–65. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467915\">https://doi.org/10.1145/3465084.3467915</a>.","apa":"Alistarh, D.-A., Töpfer, M., &#38; Uznański, P. (2021). Comparison dynamics in population protocols. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 55–65). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467915\">https://doi.org/10.1145/3465084.3467915</a>","ieee":"D.-A. Alistarh, M. Töpfer, and P. Uznański, “Comparison dynamics in population protocols,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 55–65."},"date_updated":"2023-08-11T10:56:04Z","doi":"10.1145/3465084.3467915","scopus_import":"1","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"date_created":"2021-08-22T22:01:20Z","date_published":"2021-07-21T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","title":"Comparison dynamics in population protocols","acknowledgement":"We would like to thank Rati Gelashvili for very useful discussions, and the PODC anonymous reviewers for their careful reading of our paper, and for their useful remarks. This work is partially supported by the Polish National Science Center (NCN) grant UMO2017/25/B/ST6/02010.","oa_version":"None","external_id":{"isi":["000744439800005"]},"isi":1,"page":"55-65","quality_controlled":"1","status":"public","year":"2021","_id":"9951","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450385480"]},"month":"07"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"has_accepted_license":"1","month":"07","_id":"9952","year":"2021","status":"public","quality_controlled":"1","oa_version":"Published Version","title":"Three-dimensional geometry controls division symmetry in stem cell colonies","acknowledgement":"We would like to thank the entire Paluch and Baum laboratories at the MRC-LMCB and the Chalut lab at the Cambridge SCI for discussions and feedback throughout the project, and the MRC-LMCB microscopy platform, in particular Andrew Vaughan, for technical support.","isi":1,"external_id":{"isi":["000681395800008"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","file":[{"relation":"main_file","file_size":8651724,"date_updated":"2021-08-23T07:32:20Z","content_type":"application/pdf","file_id":"9954","access_level":"open_access","date_created":"2021-08-23T07:32:20Z","success":1,"checksum":"f086f9d7cb63b2474c01921cb060c513","file_name":"2021_JournalOfCellScience_Chaigne.pdf","creator":"asandaue"}],"date_created":"2021-08-22T22:01:20Z","date_published":"2021-07-01T00:00:00Z","department":[{"_id":"EdHa"}],"ddc":["570"],"scopus_import":"1","publisher":"The Company of Biologists","oa":1,"date_updated":"2025-07-10T12:02:07Z","intvolume":"       134","doi":"10.1242/jcs.255018","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_number":"jcs255018","citation":{"chicago":"Chaigne, Agathe, Matthew B. Smith, R. L. Cavestany, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” <i>Journal of Cell Science</i>. The Company of Biologists, 2021. <a href=\"https://doi.org/10.1242/jcs.255018\">https://doi.org/10.1242/jcs.255018</a>.","ama":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. Three-dimensional geometry controls division symmetry in stem cell colonies. <i>Journal of Cell Science</i>. 2021;134(14). doi:<a href=\"https://doi.org/10.1242/jcs.255018\">10.1242/jcs.255018</a>","mla":"Chaigne, Agathe, et al. “Three-Dimensional Geometry Controls Division Symmetry in Stem Cell Colonies.” <i>Journal of Cell Science</i>, vol. 134, no. 14, jcs255018, The Company of Biologists, 2021, doi:<a href=\"https://doi.org/10.1242/jcs.255018\">10.1242/jcs.255018</a>.","ista":"Chaigne A, Smith MB, Cavestany RL, Hannezo EB, Chalut KJ, Paluch EK. 2021. Three-dimensional geometry controls division symmetry in stem cell colonies. Journal of Cell Science. 134(14), jcs255018.","short":"A. Chaigne, M.B. Smith, R.L. Cavestany, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Journal of Cell Science 134 (2021).","ieee":"A. Chaigne, M. B. Smith, R. L. Cavestany, E. B. Hannezo, K. J. Chalut, and E. K. Paluch, “Three-dimensional geometry controls division symmetry in stem cell colonies,” <i>Journal of Cell Science</i>, vol. 134, no. 14. The Company of Biologists, 2021.","apa":"Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, E. B., Chalut, K. J., &#38; Paluch, E. K. (2021). Three-dimensional geometry controls division symmetry in stem cell colonies. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.255018\">https://doi.org/10.1242/jcs.255018</a>"},"volume":134,"publication":"Journal of Cell Science","type":"journal_article","issue":"14","publication_status":"published","day":"01","fulldoi":"https://doi.org/10.1242/jcs.255018","file_date_updated":"2021-08-23T07:32:20Z","abstract":[{"text":"Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry.","lang":"eng"}],"article_type":"original","author":[{"last_name":"Chaigne","first_name":"Agathe","full_name":"Chaigne, Agathe"},{"first_name":"Matthew B.","full_name":"Smith, Matthew B.","last_name":"Smith"},{"last_name":"Cavestany","full_name":"Cavestany, R. L.","first_name":"R. L."},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"},{"last_name":"Chalut","full_name":"Chalut, Kevin J.","first_name":"Kevin J."},{"last_name":"Paluch","full_name":"Paluch, Ewa K.","first_name":"Ewa K."}]}]